Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 9
Found at i:302906 original size:32 final size:32
Alignment explanation
Indices: 302865--302965 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
302855 GGCAGTAACT
*
302865 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
302897 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
302929 TACATTGTATTGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
302962 TACA
1 TACA
302966 AATCATTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:302907 original size:13 final size:13
Alignment explanation
Indices: 302889--302945 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
302879 ACAAAACTTA
302889 TGTATCGATACAT
1 TGTATCGATACAT
302902 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
302920 ATGTATCGATACAT
1 -TGTATCGATACAT
*
302934 TGTATTGATACA
1 TGTATCGATACA
302946 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:303309 original size:20 final size:19
Alignment explanation
Indices: 303284--303339 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
303274 GTTGGGCACA
303284 ATGTATCGATACTTTTCACC
1 ATGTATCGATACTTTTC-CC
* * *
303304 ATGTATTGATACAATGTCCC
1 ATGTATCGATAC-TTTTCCC
303324 ATGTATCGATACTTTT
1 ATGTATCGATACTTTT
303340 TACTTAGGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACTTTTCCC
Found at i:306753 original size:3 final size:3
Alignment explanation
Indices: 306745--306783 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
306735 GTAAACCATG
306745 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
306784 TTCAAATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:308436 original size:98 final size:97
Alignment explanation
Indices: 308218--308465 Score: 268
Period size: 98 Copynumber: 2.5 Consensus size: 97
308208 AATTTTATTT
* * * * *
308218 ATCAGGGATACTCCAACCCTATTCTTCCAAGGGGATACTCCAACCCTGCTTTTAAACACATCAAA
1 ATCAGGGACACTCCAACCCCATTCATCCGAGGGGATACTCCAACCCTGTTTTTAAACACATCAAA
* *
308283 GTTTAAATCTTATTCTCACTTAAATTGTCACC
66 GTTTAAATCTTATTCTCACCTAAATTATCACC
* * * * *
308315 ATCAGGGACATTTCAACCTCATTCCTCCGAGGGGATACTCCAACCCTGTTTTTAAA-ACTTGTC-
1 ATCAGGGACACTCCAACCCCATTCATCCGAGGGGATACTCCAACCCTGTTTTTAAACAC--ATCA
** **
308378 AAGATTTGAAA-CTTATTCTTGCCTAAATTATCATT
64 AAG-TTT-AAATCTTATTCTCACCTAAATTATCACC
* * *
308413 GTCGGGGACACTCCAACCCCATTCATCCGAGGGGATACTCCAACCCCGTTTTT
1 ATCAGGGACACTCCAACCCCATTCATCCGAGGGGATACTCCAACCCTGTTTTT
308466 CAATCAAAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
96 2 0.02
97 51 0.41
98 69 0.55
99 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (97 bp):
ATCAGGGACACTCCAACCCCATTCATCCGAGGGGATACTCCAACCCTGTTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACCTAAATTATCACC
Found at i:309973 original size:21 final size:21
Alignment explanation
Indices: 309947--310017 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
309937 AGTTCAGGAT
309947 TGAATGTATCGATACGTTGCA
1 TGAATGTATCGATACGTTGCA
309968 TGAATGTATCGATACGTTGCA
1 TGAATGTATCGATACGTTGCA
* *
309989 TGAATTTATCGATACGTTACA
1 TGAATGTATCGATACGTTGCA
310010 TGAATGTA
1 TGAATGTA
310018 GCTATGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (21 bp):
TGAATGTATCGATACGTTGCA
Found at i:310073 original size:20 final size:20
Alignment explanation
Indices: 310044--310114 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
310034 AATCTTAATT
310044 TATATCGATACATATCAAAA
1 TATATCGATACATATCAAAA
* *
310064 TATATTGATACA-ATACACAA
1 TATATCGATACATAT-CAAAA
* ** *
310084 TGTATTAATACATATAAAAA
1 TATATCGATACATATCAAAA
*
310104 TGTATCGATAC
1 TATATCGATAC
310115 TCTGAGCTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.05
20 37 0.90
21 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (20 bp):
TATATCGATACATATCAAAA
Found at i:313379 original size:28 final size:28
Alignment explanation
Indices: 313248--313519 Score: 165
Period size: 28 Copynumber: 9.7 Consensus size: 28
313238 TATTAAAAGT
*** * **
313248 AAGCCCACATTAGCTAGCTTTTAAATTG
1 AAGCCCACATTAGCTAGCACCTAAGTCA
* * *
313276 AAGCCCATATTAGCTAGCTTCC-AAGTTA
1 AAGCCCACATTAGCTAGC-ACCTAAGTCA
* *
313304 AAGCTCACATTAGCTAGCACTTAAGTCA
1 AAGCCCACATTAGCTAGCACCTAAGTCA
* *
313332 AAGCCCACATTAGTTGGCACCTAAGTCA
1 AAGCCCACATTAGCTAGCACCTAAGTCA
* * * *
313360 AAGCTCACATTAGCTAGCACCCAAATTTA
1 AAGCCCACATTAGCTAGCA-CCTAAGTCA
* * * *
313389 AAGCCCATAATT-GTTGGCACCCT-AGTCG
1 AAGCCCA-CATTAGCTAGCA-CCTAAGTCA
* * * * * *
313417 AAGCTCATACTAGCTAGTACCTGAGTCG
1 AAGCCCACATTAGCTAGCACCTAAGTCA
* * * * *
313445 AAGCCCACACTAGTTGGCACCTGATTCA
1 AAGCCCACATTAGCTAGCACCTAAGTCA
*
313473 AAGCCCACATTAACT-GCACCTAAGTCA
1 AAGCCCACATTAGCTAGCACCTAAGTCA
* *
313500 AAGCCTATATTAGCTAGCAC
1 AAGCCCACATTAGCTAGCAC
313520 GTGAATCAAG
Statistics
Matches: 188, Mismatches: 49, Indels: 14
0.75 0.20 0.06
Matches are distributed among these distances:
27 28 0.15
28 136 0.72
29 21 0.11
30 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (28 bp):
AAGCCCACATTAGCTAGCACCTAAGTCA
Found at i:313421 original size:57 final size:56
Alignment explanation
Indices: 313298--313504 Score: 186
Period size: 56 Copynumber: 3.7 Consensus size: 56
313288 GCTAGCTTCC
* ** *
313298 AAGTTAAAGCTCACATTAGCTAGCACTTAAGTCAAAGCCCACATTAGTTGGCACCT
1 AAGTCAAAGCTCACATTAGCTAGCACCAAAGTCAAAGCCCAAATTAGTTGGCACCT
* *
313354 AAGTCAAAGCTCACATTAGCTAGCACCCAAATTTAAAGCCCATAATT-GTTGGCACCCT
1 AAGTCAAAGCTCACATTAGCTAGCA-CCAAAGTCAAAGCCCA-AATTAGTTGGCA-CCT
* * * * ** * * *
313412 -AGTCGAAGCTCATACTAGCTAGTACCTGAGTCGAAGCCCACACTAGTTGGCACCT
1 AAGTCAAAGCTCACATTAGCTAGCACCAAAGTCAAAGCCCAAATTAGTTGGCACCT
* * * * *
313467 GATTCAAAGCCCACATTAACT-GCACCTAAGTCAAAGCC
1 AAGTCAAAGCTCACATTAGCTAGCACCAAAGTCAAAGCC
313505 TATATTAGCT
Statistics
Matches: 120, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
55 19 0.16
56 56 0.47
57 39 0.32
58 6 0.05
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (56 bp):
AAGTCAAAGCTCACATTAGCTAGCACCAAAGTCAAAGCCCAAATTAGTTGGCACCT
Found at i:313556 original size:28 final size:27
Alignment explanation
Indices: 313461--313557 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
313451 ACACTAGTTG
* * * *
313461 GCACCTGATTCAAAGCCCACATTAACT
1 GCACCTAAGTCAAAGCCTACAGTAACT
* * *
313488 GCACCTAAGTCAAAGCCTATATTAGCT
1 GCACCTAAGTCAAAGCCTACAGTAACT
* *
313515 AGCACGTGAA-TCAAGGCCTACAGTAACT
1 -GCACCT-AAGTCAAAGCCTACAGTAACT
313543 GCCACCTAAGTCAAA
1 G-CACCTAAGTCAAA
313558 TTGCATATTA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
27 25 0.46
28 27 0.50
29 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (27 bp):
GCACCTAAGTCAAAGCCTACAGTAACT
Found at i:314155 original size:2 final size:2
Alignment explanation
Indices: 314148--314172 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
314138 AACAATTTTA
314148 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
314173 AAAAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:314206 original size:4 final size:4
Alignment explanation
Indices: 314186--314229 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
314176 AATTATGTGT
*
314186 TAAA -AAA T-AA T-AA TAAA TAAA AAAA TAAA TAAA -AAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
314230 AGCATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 12 0.34
4 23 0.66
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:314214 original size:12 final size:12
Alignment explanation
Indices: 314197--314230 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
314187 AAAAAATAAT
314197 AATAAATAAAAA
1 AATAAATAAAAA
314209 AATAAAT-AAAA
1 AATAAATAAAAA
314220 AATAAATAAAA
1 AATAAATAAAA
314231 GCATAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:314216 original size:19 final size:18
Alignment explanation
Indices: 314187--314230 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
314177 ATTATGTGTT
*
314187 AAAAAATAATAATAAATA
1 AAAAAATAATAAAAAATA
314205 AAAAAATAAATAAAAAATA
1 AAAAAAT-AATAAAAAATA
314224 AATAAAA
1 AA-AAAA
314231 GCATAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAATAATAAAAAATA
Found at i:321577 original size:14 final size:15
Alignment explanation
Indices: 321560--321596 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
321550 AATTTTTTAA
321560 TTTTTTAAATAT-AT
1 TTTTTTAAATATAAT
*
321574 TTTTTAAAATATAAT
1 TTTTTTAAATATAAT
321589 TTTTTTAA
1 TTTTTTAA
321597 TTCGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTAAATATAAT
Found at i:321708 original size:18 final size:18
Alignment explanation
Indices: 321681--321722 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
321671 TCAATTCTCT
* *
321681 ATTAATTTTTATAAATTA
1 ATTAAATTTTAAAAATTA
321699 ATTAAATTTTAAAAATTA
1 ATTAAATTTTAAAAATTA
321717 A-TAAAT
1 ATTAAAT
321723 AATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTAAATTTTAAAAATTA
Found at i:322021 original size:22 final size:22
Alignment explanation
Indices: 321984--322030 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
321974 AATTGTTATT
321984 ATAATTTTAATAAAA-TAAAAA
1 ATAATTTTAATAAAATTAAAAA
*
322005 ATAATATTTAATTAAATTTAAAAA
1 ATAAT-TTTAA-TAAAATTAAAAA
322029 AT
1 AT
322031 TTACATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 5 0.23
23 4 0.18
24 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTTTAATAAAATTAAAAA
Found at i:322043 original size:125 final size:128
Alignment explanation
Indices: 321747--322368 Score: 750
Period size: 125 Copynumber: 4.9 Consensus size: 128
321737 TATTTTTAAT
* *
321747 AAAATAATATTTAAGTAAGTTTAAAAAAATTTACATTAATAAATTAAAATATTAA-T-TTATTAT
1 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTATT-T
321810 TTTTA-AAAAAAT-AAAAATTTAAATCAAAAATAAAAAAGATTTTTTATTATTA-TTTTTAATAA
65 TTTTATAAAAAATAAAAAATTT---T--AAAATAAAAAA-ATTTTTTATTATTAGTTTTTAATAA
321872 AATAA
124 AATAA
321877 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATT-ACAAATTAAAAATATT-ATTATTATTT
1 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATT-AAAATATTAATTATTATTT
* *
321940 TTTTATAAAAATATAAAAAATTTTAAAATAAAAAAA-TTGTTATTA-TA-ATTTTAATAAAATAA
65 TTTTATAAAAA-ATAAAAAATTTTAAAATAAAAAAATTTTTTATTATTAGTTTTTAATAAAATAA
* * *
322002 AAAATAATATTTAATTAAATTT-AAAAAATTTACATTAACAAA-TAAAATATTAATCATTATATT
1 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTATTTT
* * * *
322065 TTT-T---AAATAAAAAATTTTAAATAAAAAAAAAGTTTATTATTATTATTTTTTGATAAAATAA
66 TTTATAAAAAATAAAAAATTTTAAA-ATAAAAAAA-TTTTTTATTATTAGTTTTTAATAAAATAA
* *
322126 AAAATAATATTTAATTACGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTATGTT
1 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTATTTT
322191 TTTAT-AAAAATAAAAAATTTAAATTATTATAATAAAAAAATATTTTTATTA-TAGTTTTTAATA
66 TTTATAAAAAATAAAAAA-TT---TTA--A-AATAAAAAAAT-TTTTTATTATTAGTTTTTAATA
322254 AAATAA
123 AAATAA
322260 AAAATAATATTTAATTAAGTTT-AAAAAATTTACATTAACAAATTAAAATATTAATTATTATATC
1 AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTAT-T-
*
322324 TTTTT-T--AAAAT-AAAAATTTTAAATTAAAAAAAGGTTTTTTATTAT
64 TTTTTATAAAAAATAAAAAATTTTAAAATAAAAAAA--TTTTTTATTAT
322369 AATAATAATT
Statistics
Matches: 439, Mismatches: 22, Indels: 65
0.83 0.04 0.12
Matches are distributed among these distances:
119 15 0.03
120 10 0.02
122 8 0.02
123 11 0.03
124 60 0.14
125 71 0.16
126 40 0.09
127 3 0.01
128 14 0.03
129 17 0.04
130 54 0.12
131 12 0.03
132 7 0.02
133 55 0.13
134 39 0.09
135 22 0.05
136 1 0.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (128 bp):
AAAATAATATTTAATTAAGTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTATTTT
TTTATAAAAAATAAAAAATTTTAAAATAAAAAAATTTTTTATTATTAGTTTTTAATAAAATAA
Found at i:322093 original size:15 final size:14
Alignment explanation
Indices: 322065--322092 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
322055 TCATTATATT
322065 TTTTAAATAAAAAA
1 TTTTAAATAAAAAA
322079 TTTTAAATAAAAAA
1 TTTTAAATAAAAAA
322093 AAAGTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTTAAATAAAAAA
Found at i:323128 original size:161 final size:162
Alignment explanation
Indices: 322855--323164 Score: 421
Period size: 161 Copynumber: 1.9 Consensus size: 162
322845 TATTAGATTG
* * * *
322855 CAAGAAATAGACTTATGCATGGATTGAAATTTGAAAGATAAGACTAATACATAGAATCTGTTTTA
1 CAAGAAATAGACTTATGCATGAATTAAAATTTAAAAGATAAGACTAATACATAGAATATGTTTTA
* *
322920 AAATAAATGTGATTAATGCATAGATTGCTGATGAGAATCAGATTCTTTCTTATATAAAAGAAA-T
66 AAATAAATGTGATTAATGCATAGATTACTGATGAGAATCAGATTCTTTCTGATATAAAA-AAAGT
322984 TAATAAGACTAATACATGATGCATGTCAGACTA
130 TAATAAGACTAATACATGATGCATGTCAGACTA
* * * ** *
323017 CAAGGAATAGA-TTAATGCATGAATTAAAATTTAAAAGATGA-ATTAATGTATAGATTATGTTTT
1 CAAGAAATAGACTT-ATGCATGAATTAAAATTTAAAAGATAAGACTAATACATAGAATATGTTTT
* *
323080 AAAATAAATGTGATTAATGCATAGATTACTGATGGGAAT-TGAATTCTTTCTGATATAAAAAAAG
65 AAAATAAATGTGATTAATGCATAGATTACTGATGAGAATCAG-ATTCTTTCTGATATAAAAAAAG
* *
323144 TTGATAAGACTAATGCATGAT
129 TTAATAAGACTAATACATGAT
323165 ACATAGATTT
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
160 4 0.03
161 92 0.71
162 33 0.26
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (162 bp):
CAAGAAATAGACTTATGCATGAATTAAAATTTAAAAGATAAGACTAATACATAGAATATGTTTTA
AAATAAATGTGATTAATGCATAGATTACTGATGAGAATCAGATTCTTTCTGATATAAAAAAAGTT
AATAAGACTAATACATGATGCATGTCAGACTA
Found at i:323443 original size:96 final size:93
Alignment explanation
Indices: 323304--323672 Score: 382
Period size: 84 Copynumber: 4.0 Consensus size: 93
323294 TTTTTATAGG
* * *
323304 AAAAA-AAAAGTTGATTGATTACAAATGTCAAACTGTAAGGATTAGACTAATACATGAATTATAT
1 AAAAAGAAAAGTTGATTGAATATAAATGTCAAACTGTAAGGATTAGACTAATGCATGAATTATAT
323368 CTGAAAATCGGATTATTTTTTATTAAAAAA
66 CTGAAAATCGGATT-TTTTTTA-TAAAAAA
* * * *
323398 AAAAGAGAAAAGTTGATTGAATATAAATATTAGACTGTAAAGATTAGACTAATGCATGAATTATA
1 AAAA-AGAAAAGTTGATTGAATATAAATGTCAAACTGTAAGGATTAGACTAATGCATGAATTATA
* * ** *
323463 TTTG-ACATCAAATTCTTTTTTATAGAAAA
65 TCTGAAAATCGGATT-TTTTTTATAAAAAA
* * * * * *
323492 AAAAAGAAAAGTTGATTGAGTGTAAATGTCAAATTGCAAGGGTTAGATTAATGCATGAATTATAT
1 AAAAAGAAAAGTTGATTGAATATAAATGTCAAACTGTAAGGATTAGACTAATGCATGAATTATAT
*
323557 CTGAGAATCGGA-TTTTTTTAT------
66 CTGAAAATCGGATTTTTTTTATAAAAAA
* * **
323578 -AAAA-AAAAGTTGATTGAATGTAAATGTCAAACTGTAAGGATTGGACTAATGTGTGAATTATAT
1 AAAAAGAAAAGTTGATTGAATATAAATGTCAAACTGTAAGGATTAGACTAATGCATGAATTATAT
* * *
323641 TTGAGAATCGGATTCTTTTTTATAGAAAA
66 CTGAAAATCGGATT-TTTTTTATAAAAAA
323670 AAA
1 AAA
323673 CTAGAAGGAT
Statistics
Matches: 226, Mismatches: 37, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
84 62 0.27
85 5 0.02
86 8 0.04
92 8 0.04
93 56 0.25
94 18 0.08
95 15 0.07
96 54 0.24
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (93 bp):
AAAAAGAAAAGTTGATTGAATATAAATGTCAAACTGTAAGGATTAGACTAATGCATGAATTATAT
CTGAAAATCGGATTTTTTTTATAAAAAA
Found at i:323524 original size:189 final size:177
Alignment explanation
Indices: 323261--323672 Score: 472
Period size: 189 Copynumber: 2.3 Consensus size: 177
323251 AAAATTAAAT
* * * *
323261 TAATGCATGAATGATATGTGAGCATCAGATTCTTTTTTATAG---GAAAAAAAAAGTTGATTGAT
1 TAATGCATGAATTATATTTGAGCATCAGATTCTTTTTTATAGAAAAAAAAAAAAAGTTGATTGAG
*
323323 TACAAATGTCAAACTGTAAGGATTAGACTAATACATGAATTATATCTGAAAATCGGATTATTTTT
66 TACAAATGTCAAACTGCAAGGATTAGACTAATACATGAATTATATCTGAAAATCGGA-T-TTTTT
* *
323388 TATTAAAAAAAAAAGAGAAAAGTTGATTGAATATAAATATTAGACTGTAAAGATTAGAC
129 TA-T-------AAA-A-AAAAGTTGATTGAATATAAATATCAAACTGTAAAGATTAGAC
*
323447 TAATGCATGAATTATATTTGA-CATCAAATTCTTTTTTATAGAAAAAAAAAGAAAAGTTGATTGA
1 TAATGCATGAATTATATTTGAGCATCAGATTCTTTTTTATAGAAAAAAAAA-AAAAGTTGATTGA
** * * * * *
323511 GTGTAAATGTCAAATTGCAAGGGTTAGATTAATGCATGAATTATATCTGAGAATCGGATTTTTTT
65 GTACAAATGTCAAACTGCAAGGATTAGACTAATACATGAATTATATCTGAAAATCGGATTTTTTT
* * * *
323576 ATAAAAAAAAGTTGATTGAATGTAAATGTCAAACTGTAAGGATTGGAC
130 ATAAAAAAAAGTTGATTGAATATAAATATCAAACTGTAAAGATTAGAC
** * *
323624 TAATGTGTGAATTATATTTGAGAATCGGATTCTTTTTTATAGAAAAAAA
1 TAATGCATGAATTATATTTGAGCATCAGATTCTTTTTTATAGAAAAAAA
323673 CTAGAAGGAT
Statistics
Matches: 197, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
177 55 0.28
178 25 0.13
179 3 0.02
185 19 0.10
186 20 0.10
187 7 0.04
188 6 0.03
189 62 0.31
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (177 bp):
TAATGCATGAATTATATTTGAGCATCAGATTCTTTTTTATAGAAAAAAAAAAAAAGTTGATTGAG
TACAAATGTCAAACTGCAAGGATTAGACTAATACATGAATTATATCTGAAAATCGGATTTTTTTA
TAAAAAAAAGTTGATTGAATATAAATATCAAACTGTAAAGATTAGAC
Found at i:325877 original size:33 final size:32
Alignment explanation
Indices: 325814--325881 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
325804 CCTTAACTGT
*
325814 TTGTATCGATACACAAAATATGTATTGATACA
1 TTGTATCGATACACAAAATATGTATCGATACA
*
325846 TTGTATCGATACATCCCAAA-ATGTATCGATACA
1 TTGTATCGATACA--CAAAATATGTATCGATACA
325879 TTG
1 TTG
325882 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 15 0.47
34 4 0.12
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACAAAATATGTATCGATACA
Found at i:331823 original size:10 final size:8
Alignment explanation
Indices: 331790--331815 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
331780 ATTTGATTAA
331790 ATTTTGTG
1 ATTTTGTG
331798 ATTTTGTG
1 ATTTTGTG
331806 ATTTTGTG
1 ATTTTGTG
331814 AT
1 AT
331816 GTTTTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:334508 original size:13 final size:13
Alignment explanation
Indices: 334490--334514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334480 ATAATGCACA
334490 GTATCGATACATT
1 GTATCGATACATT
334503 GTATCGATACAT
1 GTATCGATACAT
334515 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:334657 original size:33 final size:32
Alignment explanation
Indices: 334595--334662 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
334585 CCTTAACTGT
* *
334595 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATATATCGATACA
* *
334627 TTGTATCGGTACATCCCAAAATATATCGATACA
1 TTGTATCGATACA-CACAAAATATATCGATACA
334660 TTG
1 TTG
334663 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATATATCGATACA
Found at i:336495 original size:2 final size:2
Alignment explanation
Indices: 336488--336536 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
336478 AACTAGCTTT
336488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
336530 TA TA TA T
1 TA TA TA T
336537 GAGTTTTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:336996 original size:2 final size:2
Alignment explanation
Indices: 336989--337029 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
336979 CCATGGGACT
336989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
337030 TTGATTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:341406 original size:28 final size:28
Alignment explanation
Indices: 341364--341430 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
341354 ATAAGATAAG
341364 ATATAAA-ATAAAAATA-ACATAAAAATA
1 ATATAAATATAAAAATATA-ATAAAAATA
* * *
341391 ATATAAATATATAAATATATTAAAAATT
1 ATATAAATATAAAAATATAATAAAAATA
341419 ATAT-AATATAAA
1 ATATAAATATAAA
341431 TTTTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 14 0.41
28 19 0.56
29 1 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATAAATATAAAAATATAATAAAAATA
Found at i:341417 original size:19 final size:19
Alignment explanation
Indices: 341370--341429 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
341360 TAAGATATAA
* *
341370 AATAAAAATAACATAAAAAT
1 AATAAAAAT-ATATAAATAT
*
341390 AATATAAATATATAAATAT
1 AATAAAAATATATAAATAT
*
341409 ATTAAAAAT-TATATAATAT
1 AATAAAAATATATA-AATAT
341428 AA
1 AA
341430 ATTTTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.12
19 21 0.64
20 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAAATATATAAATAT
Found at i:341425 original size:33 final size:33
Alignment explanation
Indices: 341388--341508 Score: 111
Period size: 33 Copynumber: 3.6 Consensus size: 33
341378 TAACATAAAA
341388 ATAATATAAATATATAAATATATTAAAAATTAT
1 ATAATATAAATATATAAATATATTAAAAATTAT
* * *
341421 ATAATATAAATTTTTAAAT-TTTTATATAAA-TAT
1 ATAATATAAATATATAAATATATTA-A-AAATTAT
** * *
341454 ATAATATTTATAATATAATTATAATATAAAATTTAT
1 ATAATATAAAT-ATATAAATAT-AT-TAAAAATTAT
*
341490 ATAATATAAATGTATAAAT
1 ATAATATAAATATATAAAT
341509 TGACAAATCT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
32 4 0.06
33 30 0.45
34 8 0.12
35 9 0.13
36 14 0.21
37 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAATATAAATATATAAATATATTAAAAATTAT
Found at i:341478 original size:20 final size:19
Alignment explanation
Indices: 341391--341480 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
341381 CATAAAAATA
*
341391 ATATAAATATATAA-ATAT
1 ATATAAATATATAATATTT
* *
341409 AT-TAAA-A-ATTATA-TA
1 ATATAAATATATAATATTT
* * *
341424 ATATAAATTTTTAAATTTTT
1 ATATAAATATAT-AATATTT
341444 ATATAAATATATAATATTT
1 ATATAAATATATAATATTT
341463 ATAATATAAT-TATAATAT
1 AT-ATA-AATATATAATAT
341481 AAAATTTATA
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
15 5 0.09
16 6 0.11
17 4 0.08
18 3 0.06
19 10 0.19
20 22 0.42
21 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAAATATATAATATTT
Found at i:344081 original size:15 final size:15
Alignment explanation
Indices: 344061--344090 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
344051 TGTGACTTTT
344061 ATCCAAAAACAAAAC
1 ATCCAAAAACAAAAC
344076 ATCCAAAAACAAAAC
1 ATCCAAAAACAAAAC
344091 CATATAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.07
Consensus pattern (15 bp):
ATCCAAAAACAAAAC
Found at i:345327 original size:19 final size:21
Alignment explanation
Indices: 345280--345334 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
345270 AATTTCAACA
*
345280 ATTTGAATCGATACAGACAGT
1 ATTTGTATCGATACAGACAGT
*
345301 ATTTGTATCGATACATA-AGT
1 ATTTGTATCGATACAGACAGT
345321 A-TTGTATCGATACA
1 ATTTGTATCGATACA
345335 ATATATCGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 13 0.41
20 4 0.12
21 15 0.47
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTTGTATCGATACAGACAGT
Found at i:345408 original size:13 final size:13
Alignment explanation
Indices: 345390--345414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345380 ACTCAAATGT
345390 ATCGATACATTGC
1 ATCGATACATTGC
345403 ATCGATACATTG
1 ATCGATACATTG
345415 ATCTTTGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATCGATACATTGC
Found at i:346905 original size:20 final size:21
Alignment explanation
Indices: 346880--346919 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
346870 TGTTGCATGT
346880 TTAAAA-ATTATTT-TAAAATA
1 TTAAAAGATT-TTTATAAAATA
346900 TTAAAAGATTTTTATAAAAT
1 TTAAAAGATTTTTATAAAAT
346920 TTTTTACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTAAAAGATTTTTATAAAATA
Found at i:353900 original size:34 final size:33
Alignment explanation
Indices: 353829--353984 Score: 156
Period size: 34 Copynumber: 4.7 Consensus size: 33
353819 CTTTTCCAAA
* * * *
353829 AAGTCTACGACTCCATGGCA-CCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTCCTTTT
353861 AAGTCCACAACTCCGTGGCACCCTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT-CCTTTT
*
353895 AAGTCCACAACTCCGTGGCACCATTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTTCCTTTT
* * *
353928 CAAGCCCAC-ACTTTCGTGGCATCCCTTTTTCC-TGT
1 -AAGTCCACAAC-TCCGTGGCA-CCC-TTTTCCTTTT
* *
353963 AAGGCCACAACTTCGTGGCACC
1 AAGTCCACAACTCCGTGGCACC
353985 TTTAAGTCCA
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
32 17 0.16
33 16 0.15
34 62 0.58
35 6 0.06
36 6 0.06
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACCCTTTTCCTTTT
Found at i:353948 original size:68 final size:66
Alignment explanation
Indices: 353829--353987 Score: 178
Period size: 68 Copynumber: 2.4 Consensus size: 66
353819 CTTTTCCAAA
* * * * *
353829 AAGTCTACGACTCCATGGCACCTTTTCTTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTCCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTCAAGCCCACAACTCCGTGGCATCCCTTTTCCC-T
*
353893 TT
65 GT
* *
353895 AAGTCCACAACTCCGTGGCACCATTTTCCTTTTCAAGCCCAC-ACTTTCGTGGCATCCCTTTTTC
1 AAGTCCACAACTCCGTGGCACC-TTTT-CTTTTCAAGCCCACAAC-TCCGTGGCATCCCTTTTCC
353959 CTGT
63 CTGT
* *
353963 AAGGCCACAACTTCGTGGCACCTTT
1 AAGTCCACAACTCCGTGGCACCTTT
353988 AAGTCCAATA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
66 19 0.24
67 9 0.11
68 42 0.53
69 9 0.11
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.33
Consensus pattern (66 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTTCAAGCCCACAACTCCGTGGCATCCCTTTTCCCTG
T
Found at i:354099 original size:39 final size:39
Alignment explanation
Indices: 354035--354111 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
354025 ACCTTGTCTT
*
354035 TAAGACCAATGTCGCTGGCCCTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCCTGAATCAGCACATTGGCA
* * *
354074 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGC
1 TAAGACCAATATCGCTGGCCCTGAATCAGCACATTGGC
354112 GCCTTTGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCCTGAATCAGCACATTGGCA
Found at i:354151 original size:91 final size:88
Alignment explanation
Indices: 353986--355236 Score: 974
Period size: 101 Copynumber: 13.0 Consensus size: 88
353976 CGTGGCACCT
*
353986 TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGTACCTTGTCTTTAAGACCAATGTCGCT
1 TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCT
*
354051 GGCCCTGAATCAGCACATTGGCA
66 GGCCTTGAATCAGCACATTGGCA
* * * *
354074 -TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAAACCAATGT
1 TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGT
354138 CGCTGGCCTTGAATCAGCACATTGGCA
62 CGCTGGCCTTGAATCAGCACATTGGCA
* * *
354165 CCTTTAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGACACCTTGTCTTTAAGACCAATGTC
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTC
*
354230 ACTGGCCTTGAATCAGCACATTGGCA
63 GCTGGCCTTGAATCAGCACATTGGCA
*
354256 CTTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCCTGTCTTTAAGACCAATGTC
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTC
*
354321 GCTGGCCTTGAGTCAGCACATTGGCA
63 GCTGGCCTTGAATCAGCACATTGGCA
* *
354347 CCTTTAAGTCTAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAA
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAA
* *
354412 TGTCGCTAGCCTTGAATCAGCACATTGACA
59 TGTCGCTGGCCTTGAATCAGCACATTGGCA
*
354442 CCTTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTTGTCTTTAAGACCAATGT
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGT
* *
354507 CGCTGGCCTTGAATTAGCACATTGGAACCT
62 CGCTGGCCTTGAATCAGCACATTGG---CA
* *
354537 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGT
1 TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGT
*
354602 CGCTGGCCTTGAATCAGCATATTGGCACCTCA
62 CGCTGGCCTTGAATCAGCACATTGG-----CA
* * * * * *
354634 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGT
* *
354699 CGCTGGCCTTGAATCAACATATTGACGTCTTTGTCA
62 CGCTGGCCTTGAATCAGCACATT---G-----G-CA
* * * * * * **
354735 TCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAAAT
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGT
*
354800 CGCTGGCCTTGAATCAGCATATTTGCGCCTTTGTCA
62 CGCTGGCCTTGAATCAGCACA-TT--G-----G-CA
** * * * * * * * *
354836 TCTTTAAGTCCAACGTCGCTAGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAGTCCAGTAT
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGT
*
354901 CGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
62 CGCTGGCCTTGAATCAGCACATT---G-----G-CA
* * * *
354937 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAA
355002 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
59 TGTCGCTGGCCTTGAATCAGCACATTGG------CA
* * *
355038 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCGTTGTCATCTTTAAGTCCAA
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAA
355103 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
59 TGTCGCTGGCCTTGAATCAGCACATTGG------CA
* * * * *
355139 TCTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCA
1 ---TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT-G---TCTTTAAGA-CCA
*
355204 ATGTCGTTGGCCTTGAATCAGCACATTGGCA
58 ATGTCGCTGGCCTTGAATCAGCACATTGGCA
355235 TT
1 TT
355237 CTTCTCATCT
Statistics
Matches: 1040, Mismatches: 78, Indels: 85
0.86 0.06 0.07
Matches are distributed among these distances:
87 37 0.04
88 3 0.00
91 208 0.20
92 83 0.08
93 2 0.00
94 3 0.00
95 161 0.15
96 3 0.00
97 37 0.04
99 2 0.00
100 44 0.04
101 385 0.37
102 35 0.03
104 36 0.03
105 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (88 bp):
TTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCA
Found at i:354162 original size:52 final size:51
Alignment explanation
Indices: 354074--355276 Score: 1126
Period size: 52 Copynumber: 24.5 Consensus size: 51
354064 CACATTGGCA
* *
354074 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
** * *
354126 TAAAACCAATGTCGCTGGCCTTGAATCAGCACATT---G----G-CACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * * * *
354169 TAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGACACCTTG---TCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * *
354217 TAAGACCAATGTCACTGGCCTTGAATCAGCACATT-G-G-C---AC-T-TT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * *
354260 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCCTG---TCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * * *
354308 TAAGACCAATGTCGCTGGCCTTGAGTCAGCACATTGGCACCTT-TAAGTC--
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCA-TCTT
354357 TAA-T---AT-T-GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
* * * * *
354403 TAAGACCAATGTCGCTAGCCTTGAATCAGC--A------CATTGACACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * * *
354446 TAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTT-T-GTCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * * *
354495 TAAGACCAATGTCGCTGGCCTTGAATTAGCACATT---G----G-AACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
*
354538 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
* *
354590 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC---TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* *
354638 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * * *
354687 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGACGTCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCG-CCTTGTCATCTT
* * *
354739 TAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
** *
354788 TAAGTCCAAAATCGCTGGCCTTGAATCAGCATATTTGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
* * * **
354840 TAAGTCCAACGTCGCTAGCCTTGAATCAGCACATTGGTACC-T-TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* *
354889 TAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
354941 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
* *
354993 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
*
355042 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCGTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCC-TTGTCATCTT
* *
355094 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
* * *
355143 TAAGACCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTT-GTCATCTT
** * * ** *
355195 TAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTT
1 T-AAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGC-GCCTTGTCATCTT
* * * *
355248 CAAGTCTAAATGTCGCTGACCGTGAATCA
1 TAAGTC-CAATGTCGCTGGCCTTGAATCA
355277 TCACATTGAC
Statistics
Matches: 945, Mismatches: 138, Indels: 135
0.78 0.11 0.11
Matches are distributed among these distances:
43 157 0.17
44 9 0.01
45 6 0.01
46 5 0.01
47 1 0.00
48 116 0.12
49 248 0.26
50 10 0.01
51 12 0.01
52 322 0.34
53 56 0.06
54 3 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (51 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTGTCATCTT
Found at i:354772 original size:101 final size:103
Alignment explanation
Indices: 354535--355340 Score: 908
Period size: 101 Copynumber: 7.9 Consensus size: 103
354525 ACATTGGAAC
* * * *
354535 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTAAGTCCAAT
* *
354600 GTCGCTGGCCTTGAATCAGCATATTGGC-AC---CTCAT
65 ATCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
354635 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTTTAAGTCCAATA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATA
* * *
354698 TCGCTGGCCTTGAATCAACATATTGACGTCTTTGTCAT
66 TCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
* *
354736 CTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTTTAAGTCCAAAA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATA
* *
354799 TCGCTGGCCTTGAATCAGCATATTTGCGCCTTTGTCAT
66 TCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
* * * *
354837 CTTTAAGTCCAACGTCGCTAGCCTTGAATCAGCACATTGGTACC-T-TCATCTTTAAGTCCAGTA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATA
*
354900 TCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
66 TCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
* *
354938 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTAAGTCCAAT
* * *
355003 GTCGCTGGCCTTGAATCAGCACATTGGC-AC-CT-TCAT
65 ATCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
* * *
355039 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCGTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTAAGTCCAAT
* * *
355104 GTCGCTGGCCTTGAATCAGCACATTGGC-AC-CT-TCAT
65 ATCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
* * * * * **
355140 CTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCATCTTT-AAGTCCAA
* * * * *
355205 TGTCGTTGGCCTTGAATCAGCACATTGGC-ATTCTTCTCAT
64 TATCGCTGGCCTTGAATCAGCATATTGGCGACT-TTGTCAT
* * * * * * * **
355245 CTTCAAGTCTAAATGTCGCTGACCGTGAATCATCACATTGACATCCTTTTTCTCATCTTTAAACC
1 CTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CC---TTGTCATCTTTAAGTC
* * * *
355310 CAATATCGTTGGCCGTGAATCAACGTATTGG
61 CAATATCGCTGGCCTTGAATCAGCATATTGG
355341 TCCTTTTATC
Statistics
Matches: 631, Mismatches: 58, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
97 41 0.06
98 2 0.00
100 43 0.07
101 386 0.61
102 36 0.06
103 2 0.00
104 43 0.07
105 11 0.02
106 24 0.04
107 2 0.00
108 31 0.05
109 8 0.01
110 2 0.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (103 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATA
TCGCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
Found at i:355014 original size:254 final size:251
Alignment explanation
Indices: 353984--355233 Score: 1401
Period size: 254 Copynumber: 5.2 Consensus size: 251
353974 TTCGTGGCAC
* ** *
353984 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGTACC-TTG--TCTTTAAGACCAATG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTCTTTAAGTCCAATG
* *
354046 TCGCTGGCCCTGAATCAGCACATTGG-----CA----TAAGCCCAATATCGCTGGCCTTGAATCA
66 TCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
**
354102 GCATATTGGCGCCTTTGTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--
131 GCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* * * *
354165 --C--CTTTAAGTCCAATATTGTTGGCCTTGAATCAGTATATTGACACCTTG---T
196 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCAT
* * * * * *
354214 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATT-G-G-C----ACT-TTTAAGTCCAATA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTCTTTAAGTCCAATG
* * * * * *
354271 TTGCTGGCCTTGAATCAGCATATTGGCACC-CTGTCTTTAAGACCAATGTCGCTGGCCTTGAGTC
66 TCGCTGGCCTTGAATCAGCACATTGGCACCTC-ATCTTTAAGTCCAATATCGCTGGCCTTGAATC
* * * * *
354335 AGCACATTGGCACC-TT-TAAGTC--TAA-T---AT-T-GCTGGCCTTGAATCAGCATATTGGCG
130 AGCATATTGGCGCCTTTGTCA-TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
354390 CCTTTGTCATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGC--A----CA--TTGACAC
194 CC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCAT
* * * *
354443 CTTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTTG--TCTTTAAGACCAATG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTCTTTAAGTCCAATG
* *
354506 TCGCTGGCCTTGAATTAGCACATTGG-A----ACCTTTAAGTCCAATATCGCTGGCCTTGAATCA
66 TCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
* *
354566 GCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC
131 GCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* *
354631 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCAT
196 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCAT
* * *
354684 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGACGTCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTC-TCTTTAAGTCCAAT
* *
354749 GTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAAAATCGCTGGCCTTGAAT
65 GTCGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * *
354814 CAGCATATTTGCGCCTTTGTCATCTTTAAGTCCAACGTCGCTAGCCTTGAATCAGCACATTGGTA
129 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* *
354879 CCTTCATCTTTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
194 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCAT
*
354938 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTC-TCTTTAAGTCCAAT
355003 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
65 GTCGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
*
355068 CAGCATATTGGCGCCGTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
129 CAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * *
355133 CCTTCATCTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCAT
194 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCAT
** * * *
355192 CTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGC
1 CTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
355234 ATTCTTCTCA
Statistics
Matches: 866, Mismatches: 89, Indels: 105
0.82 0.08 0.10
Matches are distributed among these distances:
225 58 0.07
226 5 0.01
227 3 0.00
228 2 0.00
229 34 0.04
230 73 0.08
231 7 0.01
232 7 0.01
233 7 0.01
234 65 0.08
235 69 0.08
237 3 0.00
238 1 0.00
239 27 0.03
241 48 0.06
242 1 0.00
244 38 0.04
245 1 0.00
250 90 0.10
251 44 0.05
253 3 0.00
254 247 0.29
255 33 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (251 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCTCTTTAAGTCCAATG
TCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
GCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCAT
Found at i:356053 original size:19 final size:17
Alignment explanation
Indices: 356028--356120 Score: 76
Period size: 19 Copynumber: 5.6 Consensus size: 17
356018 ACAGTAATTG
356028 TATCGATACATAAGTGT
1 TATCGATACATAAGTGT
356045 TGCATCGAT--ATAA-TG-
1 T--ATCGATACATAAGTGT
356060 TATCGATACATAAGTGT
1 TATCGATACATAAGTGT
356077 TGCATCGATAC--AA-TG-
1 T--ATCGATACATAAGTGT
356092 TATCGATACATAAGTGTTT
1 TATCGATACATAAGTG--T
356111 TATCGATACA
1 TATCGATACA
356121 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 26
0.70 0.00 0.30
Matches are distributed among these distances:
13 14 0.23
15 8 0.13
16 8 0.13
17 8 0.13
19 24 0.39
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (17 bp):
TATCGATACATAAGTGT
Found at i:356067 original size:32 final size:32
Alignment explanation
Indices: 356026--356128 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
356016 AGACAGTAAT
*
356026 TGTATCGATACATAAGTGTTGCATCGATATAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
356058 TGTATCGATACATAAGTGTTGCATCGATACAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
**
356090 TGTATCGATACATAAGTGTTTTATCGATACAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
356122 TGTATCG
1 TGTATCG
356129 CTACGAAGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGCATCGATACAA
Found at i:356191 original size:13 final size:13
Alignment explanation
Indices: 356173--356200 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
356163 ATTACTCAAA
356173 TGTATCGATACAT
1 TGTATCGATACAT
356186 TGTATCGATACAT
1 TGTATCGATACAT
356199 TG
1 TG
356201 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:360311 original size:43 final size:43
Alignment explanation
Indices: 360260--360368 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
360250 TAACGGCATT
360260 TTTTTCATAAAATATTGCTAAATATCATAT-CCTTTAGCAGT-A
1 TTTTTCATAAAATATTGCTAAATATCA-ATGCCTTTAGCAGTGA
* ** * * *
360302 TTTCTTCATAAAATGTCACTAAAGATCAATGCCTTTAGCGGTGC
1 TTT-TTCATAAAATATTGCTAAATATCAATGCCTTTAGCAGTGA
* *
360346 TTTATCATAAAATATTGTTAAAT
1 TTTTTCATAAAATATTGCTAAAT
360369 TTTAGAGTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
42 5 0.10
43 44 0.85
44 3 0.06
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (43 bp):
TTTTTCATAAAATATTGCTAAATATCAATGCCTTTAGCAGTGA
Found at i:367180 original size:79 final size:77
Alignment explanation
Indices: 367079--367517 Score: 324
Period size: 78 Copynumber: 5.6 Consensus size: 77
367069 TTCATCTTAG
* * *
367079 GGGATACTCTAACTCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCCAACC
1 GGGATACTCCAAC-CCGTTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCTAACC
* *
367144 CCGTTATTTCTAA
65 CCATTATTTCTGA
* * *
367157 GGAGATACTCCAATCCCGTTTTTA-TTTCTAAAATATTAAATTTTTCATCT-TAGAGATACTCCA
1 GG-GATACTCCAA-CCCGTTTTTATTTTC-AAAATATTAAAATTTTCATCTCGAG-GATACTCTA
* * **
367220 A-CCCATCAATTCCAAA
62 ACCCCAT-TATTTCTGA
* * * ** * *
367236 GGGATACCCCAACCTCGCTTTTATTTCCAAAATGCTAAATTTTTCATCTCG-TGATACTCTAACC
1 GGGATACTCCAACC-CGTTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCTAACC
*
367300 CCATCAATTTC-GA
65 CCAT-TATTTCTGA
* * *
367313 GGGGATACTCTAACCCTATTTTTATTTTCAAAATATT-AAATTTT--TCTCGAGGGTACTCTAAC
1 -GGGATACTCCAACCC-GTTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCTAAC
* *
367375 CTCGTTATTT-TCGA
64 CCCATTATTTCT-GA
* * * * ** * *
367389 GTGGATACTCCAGCCCCGTTTTTATTTCCAAAAAAATCGATTTTTCATTTCGAGGATACTCTAAC
1 G-GGATACTCCA-ACCCGTTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCTAAC
* *
367454 TCTATTATTT-TCGA
64 CCCATTATTTCT-GA
**
367468 GGGGATACTCCAACCCCATTTTA-TTTCAAAAATATTAAAATTTTCATCTC
1 -GGGATACTCCAACCCGTTTTTATTTTC-AAAATATTAAAATTTTCATCTC
367518 AGAAATATTC
Statistics
Matches: 285, Mismatches: 55, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
75 10 0.04
76 40 0.14
77 30 0.11
78 109 0.38
79 94 0.33
80 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (77 bp):
GGGATACTCCAACCCGTTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCTAACCC
CATTATTTCTGA
Found at i:367492 original size:232 final size:234
Alignment explanation
Indices: 367077--367517 Score: 529
Period size: 232 Copynumber: 1.9 Consensus size: 234
367067 TTTTCATCTT
*
367077 AGGGGATACTCTAACTCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGATACTCCAA
1 AGGGGATACTCTAACTCCACTTTTATTTTCAAAATATTAAAATTTT-ATCTCGAGGATACTCCAA
* * * *
367142 CCCCGTTATTTCTAAGGAGATACTCCAATCCCGTTTTTATTTCTAAAATATTAAATTTTTCATCT
65 CCCCGTTATTTCTAAGGAGATACTCCAACCCCGTTTTTATTTCCAAAAAAATAAATTTTTCATCT
* *
367207 TAGAGATACTCCAACCCATCAATTCCAAAGGGATACCCCAACCTCGCTTTTATTTCCAAAATGCT
130 TAGAGATACTCCAACCCATCAATTCCAAAGGGATACCCCAACCTCGCTTTTATTTCAAAAATACT
*
367272 AAATTTTTCATCTCGTGATACTCTAACCCCATCAATTTCG
195 AAAATTTTCATCTCGTGATACTCTAACCCCATCAATTTCG
* * *
367312 AGGGGATACTCTAAC-CCTATTTTTATTTTCAAAATATT-AAATTTT-TCTCGAGGGTACTCTAA
1 AGGGGATACTCTAACTCC-ACTTTTATTTTCAAAATATTAAAATTTTATCTCGAGGATACTCCAA
* * * **
367374 CCTCGTTATTT-TCGAGTG-GATACTCCAGCCCCGTTTTTATTTCCAAAAAAATCGATTTTTCAT
65 CCCCGTTATTTCT-AAG-GAGATACTCCAACCCCGTTTTTATTTCCAAAAAAATAAATTTTTCAT
* * * * * * * * *
367437 -TTCGAGGATACTCTAACTCTATTATTTTCGAGGGGATACTCCAACC-C-CATTTTATTTCAAAA
128 CTTAGA-GATACTCCAAC-CCATCAATTCCAAAGGGATACCCCAACCTCGC-TTTTATTTCAAAA
*
367499 ATATTAAAATTTTCATCTC
190 ATACTAAAATTTTCATCTC
367518 AGAAATATTC
Statistics
Matches: 174, Mismatches: 26, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
231 6 0.03
232 104 0.60
233 22 0.13
234 9 0.05
235 33 0.19
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (234 bp):
AGGGGATACTCTAACTCCACTTTTATTTTCAAAATATTAAAATTTTATCTCGAGGATACTCCAAC
CCCGTTATTTCTAAGGAGATACTCCAACCCCGTTTTTATTTCCAAAAAAATAAATTTTTCATCTT
AGAGATACTCCAACCCATCAATTCCAAAGGGATACCCCAACCTCGCTTTTATTTCAAAAATACTA
AAATTTTCATCTCGTGATACTCTAACCCCATCAATTTCG
Found at i:368456 original size:19 final size:20
Alignment explanation
Indices: 368411--368461 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
368401 CTGCCAGTTT
* *
368411 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTAAA
*
368431 TATGTATCGATACAA-TAAA
1 CATGTATCGATACAATTAAA
*
368450 CATGTATTGATA
1 CATGTATCGATA
368462 TAATGTATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:370340 original size:14 final size:16
Alignment explanation
Indices: 370321--370358 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
370311 TGATGTAATC
*
370321 TTTTTTTCATTTT-T-
1 TTTTTTTAATTTTATA
370335 TTTTTTTAATTTTATA
1 TTTTTTTAATTTTATA
370351 TTTTTTTA
1 TTTTTTTA
370359 TAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTAATTTTATA
Found at i:372606 original size:21 final size:21
Alignment explanation
Indices: 372582--372624 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
372572 CCCAAAACCC
372582 AATAGCCCATTTAAAATTAAG
1 AATAGCCCATTTAAAATTAAG
372603 AATAGCCCATTTAAAATTAAG
1 AATAGCCCATTTAAAATTAAG
372624 A
1 A
372625 GAAACCACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (21 bp):
AATAGCCCATTTAAAATTAAG
Found at i:376898 original size:13 final size:14
Alignment explanation
Indices: 376869--376902 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
376859 ATTTAATTTA
376869 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
376883 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
376896 TTAATAA
1 TTAATAA
376903 AATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:377359 original size:21 final size:22
Alignment explanation
Indices: 377333--377385 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
377323 TTTAAATTAA
377333 TTTAAATTTAAATT-ATTAAAT
1 TTTAAATTTAAATTAATTAAAT
* *
377354 TTTAAAGTTAAATTAATTTAAT
1 TTTAAATTTAAATTAATTAAAT
*
377376 TTAAAATTTA
1 TTTAAATTTA
377386 CAGTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAAATTTAAATTAATTAAAT
Found at i:377383 original size:16 final size:16
Alignment explanation
Indices: 377316--377379 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
377306 ACATCCAAAT
*
377316 ATTTATATTTAAATTA
1 ATTTAAATTTAAATTA
377332 ATTTAAATTTAAATT-
1 ATTTAAATTTAAATTA
377347 A-TTAAATTTTAAAGTTA
1 ATTTAAA-TTTAAA-TTA
* *
377364 AATT-AATTTAATTTA
1 ATTTAAATTTAAATTA
377379 A
1 A
377380 AATTTACAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 5 0.12
15 11 0.26
16 21 0.50
17 3 0.07
18 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTTAAATTTAAATTA
Found at i:377443 original size:15 final size:15
Alignment explanation
Indices: 377423--377456 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
377413 CCTTTTAGAT
377423 ATTTAAATTAAAATA
1 ATTTAAATTAAAATA
* *
377438 ATTTAAATTTAAATT
1 ATTTAAATTAAAATA
377453 ATTT
1 ATTT
377457 TAAGAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAAAATA
Found at i:378075 original size:23 final size:23
Alignment explanation
Indices: 378040--378083 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
378030 TTTATAAAAA
378040 TTAAAATATATTAAATATAATTTT
1 TTAAAATATATTAAATA-AATTTT
*
378064 TTAAAATA-ATTATATAAATT
1 TTAAAATATATTAAATAAATT
378084 AATTATACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAATATATTAAATAAATTTT
Found at i:378522 original size:5 final size:5
Alignment explanation
Indices: 378512--378565 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
378502 TGATGATGTA
* *
378512 AATAT AATAT -ATTT AATA- AATAT AAAAAT AATAT AATA- AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
*
378560 TATAT A
1 AATAT A
378566 TTTAAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 11 0.28
5 24 0.62
6 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:378537 original size:24 final size:23
Alignment explanation
Indices: 378512--378575 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 23
378502 TGATGATGTA
378512 AATATAATATATTTAATAAATAT
1 AATATAATATATTTAATAAATAT
*
378535 AA-A-AATA-ATATAATAAATAT
1 AATATAATATATTTAATAAATAT
*
378555 AATATTATATATTTAAATAAA
1 AATATAATATATTT-AATAAA
378576 ATTAATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 14 0.41
21 5 0.15
22 4 0.12
23 5 0.15
24 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATAATATATTTAATAAATAT
Found at i:378555 original size:9 final size:9
Alignment explanation
Indices: 378510--378558 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
378500 TATGATGATG
378510 TAAATATAA
1 TAAATATAA
* *
378519 TATATTTAA
1 TAAATATAA
378528 TAAATATAAA
1 TAAATAT-AA
*
378538 AATAATATAA
1 TA-AATATAA
378548 TAAATATAA
1 TAAATATAA
378557 TA
1 TA
378559 TTATATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 21 0.66
10 6 0.19
11 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAATATAA
Found at i:378575 original size:38 final size:38
Alignment explanation
Indices: 378510--378582 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
378500 TATGATGATG
*
378510 TAAATATAATATATTTAATAAATATAAAAATAATATAA
1 TAAATATAATATATATAATAAATATAAAAATAATATAA
* * *
378548 TAAATATAATATTATATATTTAA-ATAAAATTAATA
1 TAAATATAATA-TATATAATAAATATAAAAATAATA
378583 ATTTGTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 22 0.73
39 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (38 bp):
TAAATATAATATATATAATAAATATAAAAATAATATAA
Found at i:378971 original size:28 final size:28
Alignment explanation
Indices: 378907--378978 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
378897 ATTATAATAT
* ** *
378907 TTTTAAGTATGAAATTTTGAATTTTTTTC
1 TTTTAA-TATCAAATTACGAATTATTTTC
*
378936 -TTAAATATCAAATTACGAATTATTTTC
1 TTTTAATATCAAATTACGAATTATTTTC
378963 TTTTAATATCAAATTA
1 TTTTAATATCAAATTA
378979 TAAATTGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (28 bp):
TTTTAATATCAAATTACGAATTATTTTC
Found at i:378984 original size:28 final size:28
Alignment explanation
Indices: 378907--378984 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
378897 ATTATAATAT
* * *
378907 TTTTAAGTATGAAATTTTGAATTTTTTTC
1 TTTTAA-TATCAAATTATGAATTATTTTC
* *
378936 -TTAAATATCAAATTACGAATTATTTTC
1 TTTTAATATCAAATTATGAATTATTTTC
*
378963 TTTTAATATCAAATTATAAATT
1 TTTTAATATCAAATTATGAATT
378985 GAATTATCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 18 0.45
28 22 0.55
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.51
Consensus pattern (28 bp):
TTTTAATATCAAATTATGAATTATTTTC
Found at i:380188 original size:15 final size:15
Alignment explanation
Indices: 380168--380236 Score: 66
Period size: 16 Copynumber: 4.5 Consensus size: 15
380158 CATAATTAAC
380168 TTAAATTTAAAAAAT
1 TTAAATTTAAAAAAT
**
380183 TTAAATTTAATATGAT
1 TTAAATTTAA-AAAAT
* *
380199 TTAAACTTAAAATATT
1 TTAAATTTAAAA-AAT
*
380215 TTAAATTAAAAAAAT
1 TTAAATTTAAAAAAT
*
380230 TAAAATT
1 TTAAATT
380237 AAACAAATCA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 19 0.45
16 23 0.55
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
TTAAATTTAAAAAAT
Found at i:383601 original size:26 final size:26
Alignment explanation
Indices: 383572--383622 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
383562 TACAAACTTA
383572 TATATAAATATA-AATATATTTAAATT
1 TATATAAATATATAATAT-TTTAAATT
383598 TATATAAATATATAATATTTTAAAT
1 TATATAAATATATAATATTTTAAAT
383623 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATAAATATATAATATTTTAAATT
Found at i:383631 original size:26 final size:26
Alignment explanation
Indices: 383573--383631 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
383563 ACAAACTTAT
**
383573 ATATAAATATAAATATATTTAAATTT
1 ATATAAATATAAATATATTTAAATAA
383599 ATATAAATATATAATAT-TTTAAATAA
1 ATATAAATATA-AATATATTTAAATAA
*
383625 ATTTAAA
1 ATATAAA
383632 ACGAATAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATAAATATAAATATATTTAAATAA
Found at i:384313 original size:2 final size:2
Alignment explanation
Indices: 384306--384342 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
384296 ACCAAACACT
384306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
384343 TACTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:384715 original size:30 final size:31
Alignment explanation
Indices: 384681--384740 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
384671 TCTTAATTCA
*
384681 AATATT-TATATTATATTT-ATATATTTTATT
1 AATATTATA-ATTATATTTAAAATATTTTATT
*
384711 AATATTATAATTTTATTTAAAATATTTTAT
1 AATATTATAATTATATTTAAAATATTTTAT
384741 ATTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
AATATTATAATTATATTTAAAATATTTTATT
Found at i:384768 original size:18 final size:18
Alignment explanation
Indices: 384681--384776 Score: 65
Period size: 18 Copynumber: 5.2 Consensus size: 18
384671 TCTTAATTCA
*
384681 AATATTTATAT-TATATTT
1 AATATTTATATAAAT-TTT
*
384699 ATATATTT-TATTAATATTAT
1 A-ATATTTATA-TAA-ATTTT
*
384719 AAT-TTTATTTAAAATATTT
1 AATATTTATAT-AAAT-TTT
*
384738 TATATTTATATAAATTTT
1 AATATTTATATAAATTTT
384756 AATATATTA-ATAAATTTT
1 AATAT-TTATATAAATTTT
384774 AAT
1 AAT
384777 TTATAAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
18 28 0.45
19 23 0.37
20 9 0.15
21 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTTATATAAATTTT
Found at i:384784 original size:14 final size:14
Alignment explanation
Indices: 384709--384789 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
384699 ATATATTTTA
384709 TTAATATTAT-AATT
1 TTAAT-TTATAAATT
*
384723 TT-ATTTAAAATATT
1 TTAATTTATAA-ATT
384737 TTATATTTATATAAATT
1 TTA-A-TT-TATAAATT
384754 TTAATATATTAATAAATT
1 TT-A-AT-TT-ATAAATT
384772 TTAATTTATAAATT
1 TTAATTTATAAATT
384786 TTAA
1 TTAA
384790 AATATATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
12 3 0.05
13 3 0.05
14 18 0.32
15 2 0.04
16 3 0.05
17 10 0.18
18 17 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTTATAAATT
Found at i:384838 original size:18 final size:17
Alignment explanation
Indices: 384682--384845 Score: 61
Period size: 18 Copynumber: 9.9 Consensus size: 17
384672 CTTAATTCAA
384682 ATATTTATATTATATTTAT
1 ATATTTATATTATA--TAT
384701 ATATTT-TATTA-ATATT
1 ATATTTATATTATATA-T
*
384717 ATAATTT-TATT-TA-AA
1 AT-ATTTATATTATATAT
384732 ATATTTTATATT-TATAT
1 ATA-TTTATATTATATAT
* *
384749 AAATTT-TAATATATTAAT
1 ATATTTATATTATA-T-AT
*
384767 AAATTT-TAATT-TATA-
1 ATATTTAT-ATTATATAT
*
384782 A-ATTT-TA--AAATAT
1 ATATTTATATTATATAT
384795 ATATTTATATTATATAAT
1 ATATTTATATTATAT-AT
* * *
384813 TTTTTTATCTTATATAT
1 ATATTTATATTATATAT
384830 ATATATTATATT-TATA
1 ATAT-TTATATTATATA
384846 AAATATTTTT
Statistics
Matches: 114, Mismatches: 13, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
12 3 0.03
13 2 0.02
14 10 0.09
15 13 0.11
16 16 0.14
17 26 0.23
18 36 0.32
19 8 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATATTATATAT
Found at i:385483 original size:28 final size:30
Alignment explanation
Indices: 385435--385493 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
385425 ACATAAATCA
*
385435 TAAAAATTTAATTTTATTAAA-TAA-TTAT
1 TAAAAATTTAATTTTAATAAATTAAGTTAT
*
385463 TAAATATTT-ATTATTAATAAATTAAGTTAT
1 TAAAAATTTAATT-TTAATAAATTAAGTTAT
385493 T
1 T
385494 TACGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 15 0.58
29 3 0.12
30 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TAAAAATTTAATTTTAATAAATTAAGTTAT
Found at i:388189 original size:21 final size:22
Alignment explanation
Indices: 388150--388195 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
388140 AGCACATGTA
* *
388150 ATTTTCAATATTAAAAAAATAT
1 ATTTGCAATATTAAAAAAAAAT
388172 ATTTGCAATATT-AAAAAAAAT
1 ATTTGCAATATTAAAAAAAAAT
388193 ATT
1 ATT
388196 AGAAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTGCAATATTAAAAAAAAAT
Found at i:388192 original size:23 final size:22
Alignment explanation
Indices: 388150--388195 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
388140 AGCACATGTA
*
388150 ATTTTCAATATTAAAAAAATAT
1 ATTTGCAATATTAAAAAAATAT
388172 ATTTGCAATATTAAAAAAA-AT
1 ATTTGCAATATTAAAAAAATAT
388193 ATT
1 ATT
388196 AGAAATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTGCAATATTAAAAAAATAT
Found at i:388202 original size:21 final size:22
Alignment explanation
Indices: 388156--388202 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
388146 TGTAATTTTC
* *
388156 AATATTAAAAAAATATATTTGC
1 AATATTAAAAAAATATATTAGA
388178 AATATTAAAAAAA-ATATTAGA
1 AATATTAAAAAAATATATTAGA
388199 AATA
1 AATA
388203 ATGTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AATATTAAAAAAATATATTAGA
Found at i:388290 original size:20 final size:20
Alignment explanation
Indices: 388267--388313 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
388257 AAGATTGTTG
388267 AAATTTTTATGA-AAATATTT
1 AAATTTTTATGATAAA-ATTT
** *
388287 AAATAATTATGATAAACTTT
1 AAATTTTTATGATAAAATTT
388307 AAATTTT
1 AAATTTT
388314 GTTTGTCGTA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AAATTTTTATGATAAAATTT
Found at i:389326 original size:27 final size:27
Alignment explanation
Indices: 389296--389401 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 27
389286 ATTTCAAGAG
*
389296 AAAAGCTTAATTAAAAATTTCATACGT
1 AAAAGTTTAATTAAAAATTTCATACGT
* * ***
389323 AAAAATTTAA-TAAAAATTTTTTATATAC
1 AAAAGTTTAATTAAAAA--TTTCATACGT
* *
389351 AAAAGTTTAATTAAAAATTTTATGCGT
1 AAAAGTTTAATTAAAAATTTCATACGT
* * * *
389378 GAAAGGTTAATCAAGAATTTCATA
1 AAAAGTTTAATTAAAAATTTCATA
389402 TAACATATAT
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
26 6 0.10
27 32 0.54
28 15 0.25
29 6 0.10
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (27 bp):
AAAAGTTTAATTAAAAATTTCATACGT
Found at i:393572 original size:22 final size:23
Alignment explanation
Indices: 393540--393583 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
393530 TATATTAAAT
*
393540 TTTTTATTTTATTTCATCCATTG
1 TTTTTATTTTATGTCATCCATTG
*
393563 TTTTTA-TTTATGTCATTCATT
1 TTTTTATTTTATGTCATCCATT
393584 TAAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (23 bp):
TTTTTATTTTATGTCATCCATTG
Found at i:394723 original size:2 final size:2
Alignment explanation
Indices: 394716--394745 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
394706 TAATGATGAG
394716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
394746 TTCACAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395022 original size:27 final size:24
Alignment explanation
Indices: 394992--395053 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 24
394982 TTTTATTGCT
*
394992 TTTTTATTAGATGTTATTTATGTTGGA
1 TTTTTATTAGATGCTATTT-TGTT--A
395019 TTTTTAAGTGTAGATGCTATTTTGTTA
1 TTTTT-A-T-TAGATGCTATTTTGTTA
395046 TTTTTATT
1 TTTTTATT
395054 TTTGAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 1 0.03
27 11 0.35
28 1 0.03
29 5 0.16
30 11 0.35
ACGTcount: A:0.21, C:0.02, G:0.16, T:0.61
Consensus pattern (24 bp):
TTTTTATTAGATGCTATTTTGTTA
Found at i:395124 original size:45 final size:45
Alignment explanation
Indices: 395039--395156 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
395029 TAGATGCTAT
*
395039 TTTGTTAT-TTTTATTTTTGAAAATGCTTAAAGTGTATGGATTCTCC
1 TTTGTT-TCTTTTATTTTTG-GAATGCTTAAAGTGTATGGATTCTCC
* *
395085 TTTGTTTCTTTTATTTTTGGAATGCTTAAAGTGTGTGGATTCTCT
1 TTTGTTTCTTTTATTTTTGGAATGCTTAAAGTGTATGGATTCTCC
*
395130 TTTGTTACTTTTATTTTTGGAAATGCT
1 TTTGTTTCTTTTATTTTTGG-AATGCT
395157 CTTTATATAG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
45 43 0.65
46 23 0.35
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.55
Consensus pattern (45 bp):
TTTGTTTCTTTTATTTTTGGAATGCTTAAAGTGTATGGATTCTCC
Found at i:401532 original size:18 final size:19
Alignment explanation
Indices: 401509--401549 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
401499 ATGTTATTAA
401509 TTTTTAT-TATTTAAAAAT
1 TTTTTATATATTTAAAAAT
*
401527 TTTTTATGATATTTTAAAAT
1 TTTTTAT-ATATTTAAAAAT
401547 TTT
1 TTT
401550 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATATATTTAAAAAT
Found at i:403232 original size:25 final size:25
Alignment explanation
Indices: 403204--403260 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
403194 ATGTAAAGAG
* *
403204 AATATCATAAACATATAGGACTAAA
1 AATATCACAAACATATAAGACTAAA
*
403229 AATATCACAAATATATAAGACTAAA
1 AATATCACAAACATATAAGACTAAA
403254 AATATCA
1 AATATCA
403261 ACCTACTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (25 bp):
AATATCACAAACATATAAGACTAAA
Found at i:413166 original size:7 final size:7
Alignment explanation
Indices: 412992--413149 Score: 298
Period size: 7 Copynumber: 22.3 Consensus size: 7
412982 TTATATTATA
412992 TGGCACT
1 TGGCACT
412999 TGGCACT
1 TGGCACT
413006 TGGCACT
1 TGGCACT
413013 TGGCACT
1 TGGCACT
413020 TGGCACT
1 TGGCACT
413027 TGGCACT
1 TGGCACT
413034 TGGCACT
1 TGGCACT
413041 TGGCACT
1 TGGCACT
413048 TGGCACT
1 TGGCACT
413055 TGGCACT
1 TGGCACT
413062 TGGCACT
1 TGGCACT
413069 TGGCACT
1 TGGCACT
413076 TGGCACT
1 TGGCACT
413083 TGGCACT
1 TGGCACT
413090 TGCTGCACT
1 TG--GCACT
413099 TGGCACT
1 TGGCACT
413106 TGGCACT
1 TGGCACT
413113 TGGCACT
1 TGGCACT
413120 TGGCACT
1 TGGCACT
413127 TGGCACT
1 TGGCACT
413134 TGGCACT
1 TGGCACT
413141 TGGCACT
1 TGGCACT
413148 TG
1 TG
413150 CTGACACGTG
Statistics
Matches: 149, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
7 142 0.95
9 7 0.05
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.29
Consensus pattern (7 bp):
TGGCACT
Found at i:418547 original size:7 final size:7
Alignment explanation
Indices: 418391--418544 Score: 290
Period size: 7 Copynumber: 21.9 Consensus size: 7
418381 TTATATTATA
418391 TGGCACT
1 TGGCACT
418398 TGGCACT
1 TGGCACT
418405 TGGCACT
1 TGGCACT
418412 TGGCACT
1 TGGCACT
418419 TGGCACT
1 TGGCACT
418426 TGGCACT
1 TGGCACT
418433 TGGCACT
1 TGGCACT
418440 TGGCACT
1 TGGCACT
418447 TGGCACT
1 TGGCACT
418454 TGGCACT
1 TGGCACT
418461 TGGCACT
1 TGGCACT
418468 TGGCACT
1 TGGCACT
418475 TGGCACT
1 TGGCACT
418482 TGGCACT
1 TGGCACT
418489 TGGCACT
1 TGGCACT
418496 TGGCACT
1 TGGCACT
418503 TGGCACT
1 TGGCACT
418510 TGGCACT
1 TGGCACT
418517 TGGCACT
1 TGGCACT
418524 TGGCACT
1 TGGCACT
*
418531 TGGACACG
1 TGG-CACT
418539 TGGCAC
1 TGGCAC
418545 GTGCATGTGC
Statistics
Matches: 145, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
7 139 0.96
8 6 0.04
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (7 bp):
TGGCACT
Found at i:421862 original size:15 final size:16
Alignment explanation
Indices: 421830--421862 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
421820 ACTATCTCTT
*
421830 ATTTCTTATTGTTGAA
1 ATTTCATATTGTTGAA
421846 ATTTCATATTG-TGAA
1 ATTTCATATTGTTGAA
421861 AT
1 AT
421863 AGAATATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTCATATTGTTGAA
Found at i:423603 original size:2 final size:2
Alignment explanation
Indices: 423598--423659 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
423588 TGCCTCTCTC
* * *
423598 AT AT AT AT AT AT AT AT AT AT -T AC AC CT CAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
423640 AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
423660 ATAAGGTTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 2 0.04
2 50 0.94
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:423961 original size:21 final size:19
Alignment explanation
Indices: 423936--423986 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
423926 AGTTGAGAGA
423936 AAGAATTAAGAGAAAAGAGC
1 AAGAATTAAGAGAAAAGA-C
*
423956 AGAGAA-TAGAGAGAATAGAC
1 A-AGAATTA-AGAGAAAAGAC
423976 AAGAATTAAGA
1 AAGAATTAAGA
423987 AGATGCTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 7 0.26
20 7 0.26
21 13 0.48
ACGTcount: A:0.59, C:0.04, G:0.25, T:0.12
Consensus pattern (19 bp):
AAGAATTAAGAGAAAAGAC
Found at i:432153 original size:11 final size:12
Alignment explanation
Indices: 432126--432152 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
432116 AGGTTTCTTC
432126 TTTTCTTTTTTT
1 TTTTCTTTTTTT
432138 TTTTCTTTTTTT
1 TTTTCTTTTTTT
432150 TTT
1 TTT
432153 CAAGAACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:434387 original size:2 final size:2
Alignment explanation
Indices: 434380--434415 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
434370 TTTCTGTTGA
434380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434416 TGGTTAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439025 original size:79 final size:79
Alignment explanation
Indices: 438893--439062 Score: 259
Period size: 79 Copynumber: 2.1 Consensus size: 79
438883 ACAACGGGGC
* * *
438893 TGGAGCATCCCCTGATTATGGAAAATCGGTGTCTTGGAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGCAT-CCCTGATTATAGAAAATCGATGTCTTGAAAATAAAATCGGGGTTGGAGTATCCCCT
*
438958 CGAAAATAATAGGGT
65 CGAAAATAACAGGGT
* *
438973 TGGAGCATCCCTGATTATAGAAAATCGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTT
1 TGGAGCATCCCTGATTATAGAAAATCGATGTCTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
*
439038 GAAAATAACGGGGT
66 GAAAATAACAGGGT
*
439052 TGGAGTATCCC
1 TGGAGCATCCC
439063 CTTGAAAATA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 74 0.90
80 8 0.10
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (79 bp):
TGGAGCATCCCTGATTATAGAAAATCGATGTCTTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
GAAAATAACAGGGT
Found at i:439055 original size:28 final size:28
Alignment explanation
Indices: 439018--439091 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
439008 AAAATAAAAT
439018 CGGGGTTGGAGTATCCCCTTGAAAATAA
1 CGGGGTTGGAGTATCCCCTTGAAAATAA
439046 CGGGGTTGGAGTATCCCCTTGAAAATAA
1 CGGGGTTGGAGTATCCCCTTGAAAATAA
*
439074 CGTGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
439092 GATTGTGGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTTGAAAATAA
Found at i:439128 original size:107 final size:107
Alignment explanation
Indices: 438939--439142 Score: 277
Period size: 107 Copynumber: 1.9 Consensus size: 107
438929 GAAATAAAAT
* * *
438939 CGGGGTTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGCATCCCTGATTATAGAAAATCGATGT
1 CGGGGTTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGCATCCCCGATTATAGAAAAGCGAAGT
*
439004 TTTGAAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAA
66 TTAGAAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAA
* * * * *
439046 CGGGGTTGGAGTATCCCCTTGAAAATAA-CGTGGTTGGAGTATCCCCGATTGTGGAAAAGCGAAG
1 CGGGGTTGGAGTATCCCCTCGAAAATAATAG-GGTTGGAGCATCCCCGATTATAGAAAAGCGAAG
**
439110 CTTTAG-AAATAAGGTCGGGGTTGGAGTATCCCC
65 -TTTAGAAAATAAAATCGGGGTTGGAGTATCCCC
439143 GATTGTGAGA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 1 0.01
107 79 0.94
108 4 0.05
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGCATCCCCGATTATAGAAAAGCGAAGT
TTAGAAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAA
Found at i:439166 original size:51 final size:51
Alignment explanation
Indices: 439077--439193 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
439067 AAAATAACGT
* * **
439077 GGTTGGAGTATCCCCGATTGTGGAAAAGCGAAGCTTTAGAAATAAGGTCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAGCGAAGCTTTAGAAATAAAGCCAA
* * *
439128 GGTTGGAGTATCCCCGATTGT-GAGAAATCTATA-TTTTAGAAATAAAGCCAA
1 GGTTGGAGTATCCCCGATTGTGGA-AAAGCGA-AGCTTTAGAAATAAAGCCAA
439179 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
439194 AAGGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.04
51 54 0.95
52 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAGCGAAGCTTTAGAAATAAAGCCAA
Found at i:439213 original size:79 final size:80
Alignment explanation
Indices: 439125--439274 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 80
439115 GAAATAAGGT
* * * * *
439125 CGGGGTTGGAGTAT-CCCCGATTGTGAGAAATCT-ATATTTTAGAAATAAAGCCAAGGTTGGAGT
1 CGGGATTGGAGTATCCCCCGATTATGAAAAAT-TGATATTTTAGAAATAAAACCAAGGTTAGAGT
439188 ATCCCCAAGGAAATAA
65 ATCCCCAAGGAAATAA
* * *
439204 CGGGATTGGAGTATCCCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCGAGGTTAGAGT
1 CGGGATTGGAGTAT-CCCCCGATTATGAAAAATTGATATTTTAGAAATAAAACCAAGGTTAGAGT
439269 ATCCCC
65 ATCCCC
439275 GAGATGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 13 0.22
80 1 0.02
81 46 0.77
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (80 bp):
CGGGATTGGAGTATCCCCCGATTATGAAAAATTGATATTTTAGAAATAAAACCAAGGTTAGAGTA
TCCCCAAGGAAATAA
Found at i:442345 original size:41 final size:41
Alignment explanation
Indices: 442300--442629 Score: 261
Period size: 41 Copynumber: 7.8 Consensus size: 41
442290 GAAGGGGGCA
**
442300 TCCTGCTCTTTGAGGATTAAGG-AAAAGGAGAATAAAATAG-G
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGA-AATAAAAT-GCG
* * * *
442341 TCCTGCTCCTTGGGGACTAAGGAAAAAAGGAAATAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGG-AAAAAGGAAATAAAATGCG
* * * * *
442383 TCCTACCCTTTGAAGACAAAGGAAAAAGGAAATTAAATGTG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGCG
* * *
442424 TCCTGCTTTTTGAGGACAAAGGAAAAATGAGAATAAAGTGCG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGA-AATAAAATGCG
* * * * * *
442466 TCCTACTATTTAAGAACTAGAAGGGAAAAGAAGGAAATGAAGTGCG
1 TCCTGCTCTTTGAGGAC-A-AA-GG-AAA-AAGGAAATAAAATGCG
* * * * *
442512 TCATGCTCTTTGAGGACAAAGCAAAAAAGAAA-AAAAAGCA
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGCG
* *
442552 TCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAATGTG
1 TCCTGCTCTTTGAGGAC-AAA-GG-AAA-AAGGAAATAAAATGCG
*
442597 TCCAGCTCTTTGAGGACAAAGGAAAAAAGGAAA
1 TCCTGCTCTTTGAGGACAAAGG-AAAAAGGAAA
442630 AGGCATCATG
Statistics
Matches: 229, Mismatches: 46, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
40 20 0.09
41 70 0.31
42 56 0.24
43 18 0.08
44 13 0.06
45 23 0.10
46 25 0.11
47 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAGGAAATAAAATGCG
Found at i:442570 original size:40 final size:40
Alignment explanation
Indices: 442297--442688 Score: 159
Period size: 41 Copynumber: 9.5 Consensus size: 40
442287 AAAGAAGGGG
** * *
442297 GCATCCTGCTCTTTGAGGATTAAGGAAAAGGAGAATAAAATA
1 GCATCCTGCTCTTTGAGGACAAAGGAAAA-AAGAA-AAAAAA
* * * * *
442339 G-GTCCTGCTCCTTGGGGACTAAGGAAAAAAGGAAATAAAAT
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAA-GAAA-AAAAA
* * * * * *
442380 GCATCCTACCCTTTGAAGACAAAGGAAAAAGGAAATTAAAT
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAA-AAAAA
** * * **
442421 GTGTCCTGCTTTTTGAGGACAAAGGAAAAATGAGAATAAAGT
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAA--AGAAAAAAAA
* * * * * * **
442463 GCGTCCTACTATTTAAGAACTAGAAGGGAAAAGAAGGAAATGAAGT
1 GCATCCTGCTCTTTGAGGAC-A-AA-GGAAAA-AA-GAAA-AAAAA
* * *
442509 GCGTCATGCTCTTTGAGGACAAAGCAAAAAAGAAAAAAAA
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAA
* *
442549 GCATCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAAT
1 GCATCCTGCTCTTTGAGGAC-AAA-GGAAAA-AA-GAAA-AAAAA
** * * *
442594 GTGTCCAGCTCTTTGAGGACAAAGGAAAAAAG--GAAAAG
1 GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAA
* ** * *
442632 GCATCATGCTC-AAGAGGGCAAAGGAGAAAAAG---AAAAG
1 GCATCCTGCTCTTTGAGGACAAAGGA-AAAAAGAAAAAAAA
*
442669 GCATCTTGCTCTTTGAGGAC
1 GCATCCTGCTCTTTGAGGAC
442689 TAAAAAGTGC
Statistics
Matches: 268, Mismatches: 64, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
37 26 0.10
38 21 0.08
40 22 0.08
41 71 0.26
42 49 0.18
43 17 0.06
44 12 0.04
45 30 0.11
46 20 0.07
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (40 bp):
GCATCCTGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAAA
Found at i:442591 original size:85 final size:85
Alignment explanation
Indices: 442344--442630 Score: 296
Period size: 85 Copynumber: 3.4 Consensus size: 85
442334 AAATAGGTCC
* * * * *
442344 TGCTCCTTGGGGACTAAGGAAAAAAGGAAATAAAATGCATCCTACCCTTTGAAGAC-AAA-GG-A
1 TGCTCTTTGAGGACAAAGGAAAAAA-GAAA-AAAATGCATCCTACTCTTTGAGGACAAAAGGGAA
* *
442406 AA-AAGGAAATTAAATGTGTCC
64 AAGAAGGAAATGAAATGTGTCA
* * * * * * * *
442427 TGCTTTTTGAGGACAAAGGAAAAATGAGAATAAAGTGCGTCCTACTATTTAAGAACTAGAAGGGA
1 TGCTCTTTGAGGACAAAGGAAAAA--AGAAAAAAATGCATCCTACTCTTTGAGGAC-AAAAGGGA
* *
442492 AAAGAAGGAAATGAAGTGCGTCA
63 AAAGAAGGAAATGAAATGTGTCA
* * *
442515 TGCTCTTTGAGGACAAAGCAAAAAAGAAAAAAAAGCATCCTGCTCTTTGAGGACAAAAGGGAAAA
1 TGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAA
442580 GAAGGAAATGAAATGTGTCCA
66 GAAGGAAATGAAATGTGT-CA
*
442601 -GCTCTTTGAGGACAAAGGAAAAAAGGAAAA
1 TGCTCTTTGAGGACAAAGGAAAAAAGAAAAA
442631 GGCATCATGC
Statistics
Matches: 164, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
83 38 0.23
84 3 0.02
85 57 0.35
86 26 0.16
87 3 0.02
88 37 0.23
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (85 bp):
TGCTCTTTGAGGACAAAGGAAAAAAGAAAAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAA
GAAGGAAATGAAATGTGTCA
Found at i:442667 original size:37 final size:37
Alignment explanation
Indices: 442608--442679 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
442598 CCAGCTCTTT
442608 GAGGACAAAGGAAAAAAGGAAAAGGCATCATGCTCAA
1 GAGGACAAAGGAAAAAAGGAAAAGGCATCATGCTCAA
* *
442645 GAGGGCAAAGGAGAAAAA-GAAAAGGCATCTTGCTC
1 GAGGACAAAGGA-AAAAAGGAAAAGGCATCATGCTC
442680 TTTGAGGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.47, C:0.14, G:0.29, T:0.10
Consensus pattern (37 bp):
GAGGACAAAGGAAAAAAGGAAAAGGCATCATGCTCAA
Found at i:442910 original size:60 final size:61
Alignment explanation
Indices: 442675--443023 Score: 419
Period size: 61 Copynumber: 5.8 Consensus size: 61
442665 AAAGGCATCT
* *
442675 TGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAA--AAAGAATGTGTCC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAA-AA-GCGTCC
* *
442737 TGCACTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAAGCGTCC
1 TGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCC
* * *
442799 TGCCCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGCCTTTAAAAGGAAAAAGCGTCC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCC
* * * *
442860 TACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCA
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCC
* * * *
442920 TGCTCTTTAAGGATTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAA-G-----GCGTCC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCC
* * * * *
442975 TTCTCTTTGAGGATTGAAAAATGCCACCAACTGGTGTGGGCTTTGAAAG
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
443024 ACGTCCTACA
Statistics
Matches: 253, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
55 46 0.18
60 54 0.21
61 85 0.34
62 36 0.14
63 29 0.11
64 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCC
Found at i:442918 original size:121 final size:121
Alignment explanation
Indices: 442658--443023 Score: 431
Period size: 121 Copynumber: 3.0 Consensus size: 121
442648 GGCAAAGGAG
* * * *
442658 AAAAAGAAAAGGCATCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
1 AAAAGGAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAA
* * * *
442723 A-AAAGAATGTGTCCTGCACTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTAGGCTTT
65 AGAAA-AA-GCGTCCTACTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
442782 AAAAGGAAAAAGCGTCCTGCCCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGCCTTTAAAA
1 AAAAGGAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
442847 GGAAAAAGCGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT
66 -GAAAAAGCGTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
442903 AAAAGGAAAAGGCGTCATGCTCTTTAAGGATTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
442968 G-----GCGTCCTTCTCTTTGAGGATTGAAAAATGCCACCAACTGGTGTGGGCTTT
66 GAAAAAGCGTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
*
443019 GAAAG
1 AAAAG
443024 ACGTCCTACA
Statistics
Matches: 211, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
115 19 0.09
116 29 0.14
120 1 0.00
121 82 0.39
123 22 0.10
124 55 0.26
125 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (121 bp):
AAAAGGAAAAGGCGTCATGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
GAAAAAGCGTCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:442981 original size:55 final size:55
Alignment explanation
Indices: 442909--443030 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 55
442899 CTTTAAAAGG
* * * *
442909 AAAAGGCGTCATGCTCTTTAAGGATTGGAAAGTGCCACCAACTTATGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTAAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
* * *
442964 AAAAGGCGTCCTTCTCTTTGAGGATTGAAAAATGCCACCAACTGGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTAAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
* *
443019 GAAAGACGTCCT
1 AAAAGGCGTCCT
443031 ACACTTTGAG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (55 bp):
AAAAGGCGTCCTGCTCTTTAAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
Found at i:443038 original size:55 final size:55
Alignment explanation
Indices: 442850--443042 Score: 158
Period size: 55 Copynumber: 3.4 Consensus size: 55
442840 TTTAAAAGGA
* * **
442850 AAAAG-CGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAACTTG-TGTGGGCTTT
1 AAAAGACGTCCTACACTTTGAGGATTGAAAAATGCCACCAAC-TGATGTGGGCTTT
* * * * * * *
442903 AAAAGGAAAAGGCGTCATGCTCTTTAAGGATTGGAAAGTGCCACCAACTTATGTGGGCTTT
1 AAAA-G---A--CGTCCTACACTTTGAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
* * * *
442964 AAAAGGCGTCCTTCTCTTTGAGGATTGAAAAATGCCACCAACTGGTGTGGGCTTT
1 AAAAGACGTCCTACACTTTGAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
*
443019 GAAAGACGTCCTACACTTTGAGGA
1 AAAAGACGTCCTACACTTTGAGGA
443043 CTAAAAGGTG
Statistics
Matches: 112, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
53 4 0.04
54 1 0.01
55 62 0.55
60 18 0.16
61 27 0.24
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (55 bp):
AAAAGACGTCCTACACTTTGAGGATTGAAAAATGCCACCAACTGATGTGGGCTTT
Found at i:443143 original size:61 final size:61
Alignment explanation
Indices: 443068--443241 Score: 267
Period size: 61 Copynumber: 2.8 Consensus size: 61
443058 AGAGAGCGTT
* *
443068 CTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGAAAAGGCATC
1 CTACTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * *
443129 CTACTCTTTGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
1 CTACTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * *
443190 ATGCTCTTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 CTACTCTTTGAGGACT-AGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
443242 TGTCCTGCTT
Statistics
Matches: 102, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 70 0.69
62 32 0.31
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (61 bp):
CTACTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
Found at i:443297 original size:217 final size:210
Alignment explanation
Indices: 442857--443358 Score: 650
Period size: 217 Copynumber: 2.4 Consensus size: 210
442847 GGAAAAAGCG
*
442857 TCCTACTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCA
1 TCCTACTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC
* * * * * *
442920 TGCTCTTTAAGGATTGGAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCCTTCTCTTTGA
65 TACTCTTTGAGGACTAGAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCATGCTCTTTGA
* * *
442985 GGATTGAAAAATGCCACCAACTGGTGTGGGCTTTGAAAGACGTCCTACACTTTGAGGACTAAAAG
130 GGACTAAAAAATGCCACCAACTGGTGTGGGCTTTAAAAGACGTCCTACACTTTGAGGACTAAAAG
* *
443050 GTGAAATGAGAGAGCG
195 GTGAAAGGAGAGAGCA
* * *
443066 TTCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGAAAAGGCATCCT
1 TCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* * *
443131 ACTCTTTGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATGCTC
66 ACTCTTTGAGGACTAGAAAGTGCCACCAACTTATGTGGGCTTT------AAAAGGCGTCATGCTC
* ** * **
443196 TTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTTTTTGAGGAC
125 TTTGAGGACTAAAAAA-TGCCACCAACTGGTGTGGGCTTTAAAAGACGTCCTACACTTTGAGGAC
*
443261 TAAAGGGTGAAAGGAGAGAGCA
189 TAAAAGGTGAAAGGAGAGAGCA
* * *
443283 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGG-TTTAAAAGGAGAAGGCGTCCT
1 TCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
*
443347 ACTTTTTGAGGA
66 ACTCTTTGAGGA
443359 TTGAAAAGTG
Statistics
Matches: 252, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
209 17 0.07
210 75 0.30
211 3 0.01
216 57 0.23
217 100 0.40
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (210 bp):
TCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
ACTCTTTGAGGACTAGAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCGTCATGCTCTTTGAG
GACTAAAAAATGCCACCAACTGGTGTGGGCTTTAAAAGACGTCCTACACTTTGAGGACTAAAAGG
TGAAAGGAGAGAGCA
Found at i:443371 original size:99 final size:95
Alignment explanation
Indices: 443191--443376 Score: 225
Period size: 99 Copynumber: 1.9 Consensus size: 95
443181 AAAGGCGTCA
* *
443191 TGCTCTTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTTTTTG
1 TGCTCTTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTTTTTG
*
443256 AGGACTAAAGGGTGAAAGGAGAGAGCATCC
66 AGGACTAAAGAGTGAAAGGAGAGAGCATCC
***
443286 TGCTCTTTGAGGACT-GGGAAGTGCCACCAACTTGTGTGGG-TTTAAAAGGAGAAGGCGTCCTAC
1 TGCTCTTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCGTCCTAC
*
443349 TTTTTGAGGATTGAAA-AGTGAAAGGAGA
60 TTTTTGAGGACT-AAAGAGTGAAAGGAGA
443377 AAGTTTAGAT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
93 3 0.04
94 22 0.29
95 15 0.19
96 1 0.01
98 1 0.01
99 32 0.42
100 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (95 bp):
TGCTCTTTGAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTTTTTG
AGGACTAAAGAGTGAAAGGAGAGAGCATCC
Found at i:444363 original size:1 final size:1
Alignment explanation
Indices: 444352--444401 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
444342 CTTTTCTCTC
* * * * *
444352 TTTTTTCTTTTTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
444402 GAAAAAAGGT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:444364 original size:9 final size:9
Alignment explanation
Indices: 444335--444401 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
444325 CTTAAGCAGG
444335 TTCTTTTCTT
1 TTCTTTT-TT
444345 TTCTCTCTTTT
1 TTCT-T-TTTT
444356 TTCTTTTTT
1 TTCTTTTTT
*
444365 TT-TTGTTT
1 TTCTTTTTT
*
444373 TTGTTTTTT
1 TTCTTTTTT
*
444382 TTTTGTTTTT
1 TTCT-TTTTT
*
444392 TTGTTTTTT
1 TTCTTTTTT
444401 T
1 T
444402 GAAAAAAGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.14
9 20 0.41
10 13 0.27
11 7 0.14
12 2 0.04
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:444373 original size:17 final size:16
Alignment explanation
Indices: 444353--444402 Score: 73
Period size: 17 Copynumber: 3.0 Consensus size: 16
444343 TTTTCTCTCT
444353 TTTTTCTTTTTTTTTTG
1 TTTTT-TTTTTTTTTTG
444370 TTTTTGTTTTTTTTTTG
1 TTTTT-TTTTTTTTTTG
*
444387 TTTTTTTGTTTTTTTG
1 TTTTTTTTTTTTTTTG
444403 AAAAAAGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTG
Found at i:444380 original size:25 final size:25
Alignment explanation
Indices: 444352--444399 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
444342 CTTTTCTCTC
*
444352 TTTTTTCTTT-TTTTTTTGTTTTTG
1 TTTTTTTTTTGTTTTTTTGTTTTTG
444376 TTTTTTTTTTGTTTTTTTGTTTTT
1 TTTTTTTTTTGTTTTTTTGTTTTT
444400 TTGAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (25 bp):
TTTTTTTTTTGTTTTTTTGTTTTTG
Found at i:444402 original size:8 final size:8
Alignment explanation
Indices: 444362--444402 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
444352 TTTTTTCTTT
444362 TTTTTTTG
1 TTTTTTTG
*
444370 TTTTTGTTT
1 TTTTT-TTG
444379 TTTTTTTG
1 TTTTTTTG
444387 TTTTTTTG
1 TTTTTTTG
444395 TTTTTTTG
1 TTTTTTTG
444403 AAAAAAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:457004 original size:79 final size:79
Alignment explanation
Indices: 456844--457026 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 79
456834 TGTCCTGGAT
* *
456844 ATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGCATCCCTAATTATAGAAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGCATCCCCAATTATAGAAAA
* * *
456909 TCAGTGTTTTGAAA
66 GCAGTCTTTAGAAA
* *
456923 ATAAAATCGGGGTTGGAGTATCTCCTAGAAAATAAC-GAGGTTGGAGTATCCCCAATTAT-GAAA
1 ATAAAATCGGGGTTGGAGTATCCCCTAGAAAATAACAG-GGTTGGAGCATCCCCAATTATAG-AA
456986 AAGCGAAG-CTTTAG-AA
64 AAGC--AGTCTTTAGAAA
**
457002 ATAAGGTCGGGGTTGGAGTATCCCC
1 ATAAAATCGGGGTTGGAGTATCCCC
457027 GATTGTGAGA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 2 0.02
79 82 0.91
80 4 0.04
81 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (79 bp):
ATAAAATCGGGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGCATCCCCAATTATAGAAAA
GCAGTCTTTAGAAA
Found at i:457022 original size:51 final size:51
Alignment explanation
Indices: 456959--457078 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 51
456949 AGAAAATAAC
* *
456959 GAGGTTGGAGTATCCCCAATTATGAAAAAGCGAA-GCTTTAGAAAT-AAGGT
1 GAGGTTGGAGTATCCCCAATTATGAAAAAGC-AATACTTTAGAAATAAAGCT
* * * * * *
457009 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCT
1 -GAGGTTGGAGTATCCCCAATTATGAAAAAGCAATACTTTAGAAATAAAGCT
457061 GAGGTTGGAGTATCCCCA
1 GAGGTTGGAGTATCCCCA
457079 TGGAAATAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 2 0.04
51 51 0.89
52 4 0.07
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (51 bp):
GAGGTTGGAGTATCCCCAATTATGAAAAAGCAATACTTTAGAAATAAAGCT
Found at i:457055 original size:130 final size:129
Alignment explanation
Indices: 456931--457204 Score: 349
Period size: 130 Copynumber: 2.1 Consensus size: 129
456921 AAATAAAATC
*
456931 GGGGTTGGAGTATCTCC-TAGAAAATAACGAGG-TTGGAGTATCCCCAATTATGAAAAAGCGAA-
1 GGGGTTGGAGTATCCCCAT-GAAAATAACG-GGATTGGAGTATCCCCAATTATGAAAAA-CGAAT
* *** * *
456993 GCTTTAGAAATAAGGTCGGGGTTGGAGTATCCCCGATTG-TGAGAAATCAATATTTTAGAAATAA
63 ACTTTAGAAATAAAACCGGGGTTAGAGTATCCCCGA--GATGAAAAATCAATATTTTAGAAATAA
457057 AGCT
126 AGCT
* * ** *
457061 GAGGTTGGAGTATCCCCATGGAAATAACGGGATTGGAGTATCCCCAATTATGAAAAATTAATATT
1 GGGGTTGGAGTATCCCCATGAAAATAACGGGATTGGAGTATCCCCAATTATGAAAAACGAATACT
*
457126 TTGGAAATAAAACCGGGGTTAGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCT
66 TTAGAAATAAAACCGGGGTTAGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCT
*
457190 GGGGTTAGAGTATCC
1 GGGGTTGGAGTATCC
457205 ACGAGATGAA
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
128 1 0.01
129 45 0.36
130 78 0.62
131 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (129 bp):
GGGGTTGGAGTATCCCCATGAAAATAACGGGATTGGAGTATCCCCAATTATGAAAAACGAATACT
TTAGAAATAAAACCGGGGTTAGAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCT
Found at i:457097 original size:79 final size:79
Alignment explanation
Indices: 457009--457156 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 79
456999 GAAATAAGGT
* * * * * * *
457009 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGAGGTTGGAGTAT
1 CGGGATTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTAGAGTAT
457074 CCCCATGGAAATAA
66 CCCCATGGAAATAA
* * *
457088 CGGGATTGGAGTATCCCCAATTATGAAAAATTAATATTTTGGAAATAAAACCGGGGTTAGAGTAT
1 CGGGATTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTAGAGTAT
457153 CCCC
66 CCCC
457157 GAGATGAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
CGGGATTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACCGAGGTTAGAGTAT
CCCCATGGAAATAA
Found at i:457174 original size:50 final size:50
Alignment explanation
Indices: 457096--457219 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 50
457086 AACGGGATTG
* * * *
457096 GAGTATCCCCAATTATGAAAAATTAATATTTTGGAAATAAAACCGGGGTTA
1 GAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
* *
457147 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCTGGGGTTA
1 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
*
457197 GAGTATCCACGAGATGAAAAATC
1 GAGTATCCCCGAGATGAAAAATC
457220 TAGAAATTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
50 55 0.83
51 11 0.17
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (50 bp):
GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTA
Found at i:460014 original size:31 final size:31
Alignment explanation
Indices: 459976--460037 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
459966 CATGGTTCAT
459976 TCATGATGTCTAAGATAGACCTTCCAATATC
1 TCATGATGTCTAAGATAGACCTTCCAATATC
460007 TCATGATGTCTAAGATAGACCTTCCAATATC
1 TCATGATGTCTAAGATAGACCTTCCAATATC
460038 CTTCTAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (31 bp):
TCATGATGTCTAAGATAGACCTTCCAATATC
Found at i:466964 original size:13 final size:14
Alignment explanation
Indices: 466938--466966 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
466928 TCTGTAACAT
466938 TATAAAAAATTAAA
1 TATAAAAAATTAAA
466952 TATAAAAAA-TAAA
1 TATAAAAAATTAAA
466965 TA
1 TA
466967 ACCTCGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TATAAAAAATTAAA
Found at i:469342 original size:2 final size:2
Alignment explanation
Indices: 469280--469326 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
469270 AGTTTTTTTA
469280 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
469322 TC TC T
1 TC TC T
469327 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:472203 original size:2 final size:2
Alignment explanation
Indices: 472196--472222 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
472186 TCAATGTACT
472196 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
472223 TCCCCCCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.